Polymorphic Aβ42 fibrils adopt similar secondary structure but differ in cross-strand side chain stacking interactions within the same β-sheet.

Formation of polymorphic amyloid fibrils is a common feature in neurodegenerative diseases involving protein aggregation. In Alzheimer's disease, different fibril structures may be associated with different clinical sub-types. Structural basis of fibril polymorphism is thus important for understanding the role of amyloid fibrils in the pathogenesis and progression of these diseases. Here we studied two types of Aβ42 fibrils prepared under quiescent and agitated conditions. Quiescent Aβ42 fibrils adopt a long and twisted morphology, while agitated fibrils are short and straight, forming large bundles via lateral association. EPR studies of these two types of Aβ42 fibrils show that the secondary structure is similar in both fibril polymorphs. At the same time, agitated Aβ42 fibrils show stronger interactions between spin labels across the full range of the Aβ42 sequence, suggesting a more tightly packed structure. Our data suggest that cross-strand side chain packing interactions within the same β-sheet may play a critical role in the formation of polymorphic fibrils

Treatment as required versus regular monthly treatment in the management of neovascular age-related macular degeneration: a systematic review and meta-analysis

Background: To investigate whether treatment as required ‘pro re nata’ (PRN) versus regular monthly treatment regimens lead to differences in outcomes in neovascular age-related macular degeneration (nAMD). Regular monthly administration of vascular endothelial growth factor (VEGF) inhibitors is an established gold standard treatment, but this approach is costly. Replacement of monthly by PRN treatment can only be justified if there is no difference in patient relevant outcomes. Methods: Systematic review and meta-analysis. The intervention was PRN treatment and the comparator was monthly treatment with VEGF-inhibitors. Four bibliographic databases were searched for randomised controlled trials comparing both treatment regimens directly (head-to-head studies). The last literature search was conducted in December 2014. Risk of bias assessment was performed after the Cochrane Handbook for Systematic Reviews of Interventions. Findings: We included 3 head-to-head studies (6 reports) involving more than 2000 patients. After 2 years, the weighted mean difference in best corrected visual acuity (BCVA) was 1.9 (95% CI 0.5 to 3.3) ETDRS letters in favour of monthly treatment. Systemic adverse events were higher in PRN treated patients, but these differences were not statistically significant. After 2 years, the total number of intravitreal injections required by the patients in the PRN arms were 8.4 (95% CI 7.9 to 8.9) fewer than those having monthly treatment. The studies were considered to have a moderate risk of bias. Conclusions: PRN treatment resulted in minor but statistically significant decrease in mean BCVA which may not be clinically meaningful. There is a small increase in risk of systemic adverse events for PRN treated patients. Overall, the results indicate that an individualized treatment approach with anti-VEGF using visual acuity and OCT-guided re-treatment criteria may be appropriate for most patients with nAMD

Investigation of physiological and pathological vascular functions using engineered systems

The vasculature is a highly complex, hierarchical system that performs a variety of functions in both physiological and pathological contexts. To maintain tissue homeostasis for example, the endothelium which lines all vascular structures generates a semi-permeable barrier that controls the exchange of fluids, ions, and solutes between the blood and tissue. During phases of tissue growth and wound repair, the vasculature undergoes angiogenesis, the development of new blood vessels, to provide adequate oxygen and nutrients to the new and healing tissues. In pathological situations such as cancer, blood vessels have been demonstrated to support tumor growth and provide access to the circulatory system for metastatic progression. This dissertation focuses on elucidating new mechanisms that are involved in regulating these three dynamic functions of the vasculature. In Chapter 2, we discuss preliminary work connecting the Notch signaling pathway with the ability for endothelial cells to mechanically couple to their substrate, a property that is known to regulate endothelial barrier function. Using traditional methods in two-dimensional traction force microscopy, we observed reductions in traction stresses generated by endothelial monolayers treated with a Notch inhibitor. This was accompanied by a decrease in cell- matrix tethering through focal adhesions. In Chapter 3, we utilized an engineered model of angiogenesis to probe the role of endothelial cell contractility in the formation of new vascular sprouts. Through these studies, we established an essential role of non-muscle myosin II in maintaining multicellularity during sprout morphogenesis. And in Chapter 4, we described the adaptation of a cranial window model for studying melanoma brain metastases and demonstrated the utility of this system to monitor dynamic interactions between cancer cells and the brain vasculature. Together, the work in this dissertation provides new insights into and techniques for probing outstanding questions regarding various key functions of the vasculature.2021-02-28T00:00:00

Myosin IIA-mediated forces regulate multicellular integrity during vascular sprouting

Angiogenic sprouting is a critical process involved in vascular network formation within tissues. During sprouting, tip cells and ensuing stalk cells migrate collectively into the extracellular matrix while preserving cell-cell junctions, forming patent structures that support blood flow. Although several signaling pathways have been identified as controlling sprouting, it remains unclear to what extent this process is mechanoregulated. To address this question, we investigated the role of cellular contractility in sprout morphogenesis, using a biomimetic model of angiogenesis. Three-dimensional maps of mechanical deformations generated by sprouts revealed that mainly leader cells, not stalk cells, exert contractile forces on the surrounding matrix. Surprisingly, inhibiting cellular contractility with blebbistatin did not affect the extent of cellular invasion but resulted in cell-cell dissociation primarily between tip and stalk cells. Closer examination of cell-cell junctions revealed that blebbistatin impaired adherens-junction organization, particularly between tip and stalk cells. Using CRISPR/Cas9-mediated gene editing, we further identified NMIIA as the major isoform responsible for regulating multicellularity and cell contractility during sprouting. Together, these studies reveal a critical role for NMIIA-mediated contractile forces in maintaining multicellularity during sprouting and highlight the central role of forces in regulating cell-cell adhesions during collective motility.R01 EB000262 - NIBIB NIH HHS; R01 HL115553 - NHLBI NIH HHSPublished versio

Further insights into the allan-herndon-dudley syndrome: Clinical and functional characterization of a novel MCT8 mutation

Background. Mutations in the thyroid hormone (TH) transporter MCT8 have been identified as the cause for Allan-Herndon-Dudley Syndrome (AHDS), characterized by severe psychomotor retardation and altered TH serum levels. Here we report a novel MCT8 mutation identified in 4 generations of one family, and its functional characterization. Methods. Proband and family members were screened for 60 genes involved in X-linked cognitive impairment and the MCT8 mutation was confirmed. Functional consequences of MCT8 mutations were studied by analysis of [125I]TH transport in fibroblasts and transiently transfected JEG3 and COS1 cells, and by subcellular localization of the transporter. Results. The proband and a male cousin demonstrated clinical findings characteristic of AHDS. Serum analysis showed high T3, low rT3, and normal T4 and TSH levels in the proband. A MCT8 mutation (c.869C>T; p.S290F) was identified in the proband, his cousin, and several female carriers. Functional analysis of the S290F mutant showed decreased TH transport, metabolism and protein expression in the three cell types, whereas the S290A mutation had no effect. Interestingly, both uptake and efflux of T3 and T4 was impaired in fibroblasts of the proband, compared to his healthy brother. However, no effect of the S290F mutation was observed on TH efflux from COS1 and JEG3 cells. Immunocytochemistry showed plasma membrane localization of wild-type MCT8 and the S290A and S290F mutants in JEG3 cells. Conclusions. We describe a novel MCT8 mutation (S290F) in 4 generations of a family with Allan-Herndon-Dudley Syndrome. Functional analysis demonstrates loss-of-function of the MCT8 transporter. Furthermore, our results indicate that the function of the S290F mutant is dependent on cell context. Comparison of the S290F and S290A mutants indicates that it is not the loss of Ser but its substitution with Phe, which leads to S290F dysfunction

Graphitic carbon growth on crystalline and amorphous oxide substrates using molecular beam epitaxy

We report graphitic carbon growth on crystalline and amorphous oxide substrates by using carbon molecular beam epitaxy. The films are characterized by Raman spectroscopy and X-ray photoelectron spectroscopy. The formations of nanocrystalline graphite are observed on silicon dioxide and glass, while mainly sp2 amorphous carbons are formed on strontium titanate and yttria-stabilized zirconia. Interestingly, flat carbon layers with high degree of graphitization are formed even on amorphous oxides. Our results provide a progress toward direct graphene growth on oxide materials

Data mining approach identifies research priorities and data requirements for resolving the red algal tree of life

<p>Abstract</p> <p>Background</p> <p>The assembly of the tree of life has seen significant progress in recent years but algae and protists have been largely overlooked in this effort. Many groups of algae and protists have ancient roots and it is unclear how much data will be required to resolve their phylogenetic relationships for incorporation in the tree of life. The red algae, a group of primary photosynthetic eukaryotes of more than a billion years old, provide the earliest fossil evidence for eukaryotic multicellularity and sexual reproduction. Despite this evolutionary significance, their phylogenetic relationships are understudied. This study aims to infer a comprehensive red algal tree of life at the family level from a supermatrix containing data mined from GenBank. We aim to locate remaining regions of low support in the topology, evaluate their causes and estimate the amount of data required to resolve them.</p> <p>Results</p> <p>Phylogenetic analysis of a supermatrix of 14 loci and 98 red algal families yielded the most complete red algal tree of life to date. Visualization of statistical support showed the presence of five poorly supported regions. Causes for low support were identified with statistics about the age of the region, data availability and node density, showing that poor support has different origins in different parts of the tree. Parametric simulation experiments yielded optimistic estimates of how much data will be needed to resolve the poorly supported regions (ca. 10³to ca. 10⁴nucleotides for the different regions). Nonparametric simulations gave a markedly more pessimistic image, some regions requiring more than 2.8 10⁵nucleotides or not achieving the desired level of support at all. The discrepancies between parametric and nonparametric simulations are discussed in light of our dataset and known attributes of both approaches.</p> <p>Conclusions</p> <p>Our study takes the red algae one step closer to meaningful inclusion in the tree of life. In addition to the recovery of stable relationships, the recognition of five regions in need of further study is a significant outcome of this work. Based on our analyses of current availability and future requirements of data, we make clear recommendations for forthcoming research.</p

Exploration of Augmented Reality as an Assistive Device for Students with Dyslexia

Gemstone Team ARTAugmented Reality (AR) is a rapidly emerging technology, and its potential has not yet been fully explored. As members of Team ART, we aim to explore the use of AR as an assistive device platform for people with dyslexia, with the hopes that we could take advantage of the seamless integration of reality and computer-generated images and the attractive novelty of this up and coming platform. We began our project by surveying experts and members of the dyslexia community to determine the most helpful features and user interface for an assistive device to provide real-time feedback to users with dyslexia. Then, we developed an application on the Microsoft HoloLens to analyze users' handwritten spelling of words to provide immediate feedback. We tested the application on 19 participants in grades two through six and found that all of them improved their spelling as a result of using our device. 64.2 percent of users perceived the device to as motivating, significantly greater than the percentage of users who disliked the device. There was no significant correlation between improvement in spelling accuracy and increased motivation in regards to our device. Our novel study demonstrates that with further improvement and implementation, our application can provide assistance not only to people with dyslexia, but also to children in general

Discovering Coherent Biclusters from Gene Expression Data Using Zero-Suppressed Binary Decision Diagrams

The biclustering method can be a very useful analysis tool when some genes have multiple functions and experimental conditions are diverse in gene expression measurement. This is because the biclustering approach, in contrast to the conventional clustering techniques, focuses on finding a subset of the genes and a subset of the experimental conditions that together exhibit coherent behavior. However, the biclustering problem is inherently intractable, and it is often computationally costly to find biclusters with high levels of coherence. In this work, we propose a novel biclustering algorithm that exploits the zero-suppressed binary decision diagrams (ZBDDs) data structure to cope with the computational challenges. Our method can find all biclusters that satisfy specific input conditions, and it is scalable to practical gene expression data. We also present experimental results confirming the effectiveness of our approach

Harmonization and standardization of nucleus pulposus cell extraction and culture methods

BACKGROUND: In vitro studies using nucleus pulposus (NP) cells are commonly used to investigate disc cell biology and pathogenesis, or to aid in the development of new therapies. However, lab-to-lab variability jeopardizes the much-needed progress in the field. Here, an international group of spine scientists collaborated to standardize extraction and expansion techniques for NP cells to reduce variability, improve comparability between labs and improve utilization of funding and resources. METHODS: The most commonly applied methods for NP cell extraction, expansion, and re-differentiation were identified using a questionnaire to research groups worldwide. NP cell extraction methods from rat, rabbit, pig, dog, cow, and human NP tissue were experimentally assessed. Expansion and re-differentiation media and techniques were also investigated. RESULTS: Recommended protocols are provided for extraction, expansion, and re-differentiation of NP cells from common species utilized for NP cell culture. CONCLUSIONS: This international, multilab and multispecies study identified cell extraction methods for greater cell yield and fewer gene expression changes by applying species-specific pronase usage, 60-100 U/ml collagenase for shorter durations. Recommendations for NP cell expansion, passage number, and many factors driving successful cell culture in different species are also addressed to support harmonization, rigor, and cross-lab comparisons on NP cells worldwide